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|
// ./tests/catch2-tests [section] -s
/////////////////////// Qt includes
#include <QDebug>
#include <QString>
#include <QStringList>
#include <QDir>
/////////////////////// IsoSpec
#include <IsoSpec++/isoSpec++.h>
#include <IsoSpec++/element_tables.h>
/////////////////////// Catch2 includes
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
/////////////////////// Local includes
#include "tests-config.h"
#include "TestUtils.hpp"
#include <libXpertMass/globals.hpp>
#include <libXpertMass/Polymer.hpp>
#include <libXpertMass/CrossLink.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_1_letter_cross_link("protein-1-letter", 1);
ErrorList error_list_cross_link;
SCENARIO("Construction of a CrossLink", "[CrossLink]")
{
test_utils_1_letter_cross_link.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_cross_link.msp_polChemDef;
QString polymer_file_path =
QString("%1/polymer-sequences/%2")
.arg(TESTS_INPUT_DIR)
.arg("cyan-fluorescent-protein-no-cross-link.mxp");
GIVEN(
"A Polymer is allocated as a SPtr and then the XML file is loaded from "
"disk")
{
PolymerSPtr polymer_sp = Polymer::createSPtr(pol_chem_def_csp);
REQUIRE(polymer_sp->renderXmlPolymerFile(polymer_file_path));
REQUIRE(polymer_sp->size() == 240);
WHEN(
"A CrossLink is allocated by specifying all the params in the "
"constructor")
{
CrossLink cross_link(pol_chem_def_csp,
polymer_sp,
"CFP-chromophore",
"-H2OH2",
"This is a comment");
THEN("The data in the cross-link must be set correctly")
{
REQUIRE(cross_link.getPolymerCstSPtr() == polymer_sp);
REQUIRE(cross_link.getComment().toStdString() == "This is a comment");
REQUIRE(cross_link.getCrossLinkerName().toStdString() ==
"CFP-chromophore");
REQUIRE(
cross_link.getCrossLinkerCstSPtr()->getFormula().toStdString() ==
"-H2OH2");
}
AND_WHEN(
"Another CrossLink is allocated by copy-construction or assignment")
{
CrossLink another_cross_link(cross_link);
CrossLink other_cross_link;
other_cross_link = another_cross_link;
THEN("The new CrossLink instance have to be identical to the first one")
{
REQUIRE(other_cross_link.getPolymerCstSPtr() == polymer_sp);
REQUIRE(other_cross_link.getComment().toStdString() ==
"This is a comment");
REQUIRE(other_cross_link.getCrossLinkerName().toStdString() ==
"CFP-chromophore");
REQUIRE(other_cross_link.getCrossLinkerCstSPtr()
->getFormula()
.toStdString() == "-H2OH2");
}
}
}
}
}
SCENARIO("Construction of a CrossLink and use with a Polymer", "[CrossLink]")
{
test_utils_1_letter_cross_link.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_cross_link.msp_polChemDef;
QString polymer_file_path =
QString("%1/polymer-sequences/%2")
.arg(TESTS_INPUT_DIR)
.arg("cyan-fluorescent-protein-no-cross-link.mxp");
GIVEN(
"A Polymer is allocated as a SPtr and then the XML file is loaded from "
"disk")
{
PolymerSPtr polymer_sp = Polymer::createSPtr(pol_chem_def_csp);
REQUIRE(polymer_sp->renderXmlPolymerFile(polymer_file_path));
REQUIRE(polymer_sp->size() == 240);
WHEN("A CrossLinker is referenced from the PolChemDef by name")
{
CrossLinkerCstSPtr cross_linker_csp =
pol_chem_def_csp->getCrossLinkerCstSPtrByName("CFP-chromophore");
REQUIRE(cross_linker_csp != nullptr);
REQUIRE(cross_linker_csp->getPolChemDefCstSPtr() == pol_chem_def_csp);
THEN(
"Its masses have to be ready because the CrossLinker is in the "
"PolChemDef")
{
REQUIRE_THAT(cross_linker_csp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(-20.0262147493, 0.0000000001));
REQUIRE_THAT(cross_linker_csp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(-20.0311745907, 0.0000000001));
double mono = 1000;
double avg = 1001;
cross_linker_csp->accountMasses(mono, avg, 3);
REQUIRE_THAT(
mono,
Catch::Matchers::WithinAbs(1000 - (20.0262147493 * 3), 0.0000000001));
REQUIRE_THAT(
avg,
Catch::Matchers::WithinAbs(1001 - (20.0311745907 * 3), 0.0000000001));
}
WHEN(
"A CrossLink instance is created using that CrossLinker instance, "
"the "
"CSPtr is gotten from the raw pointer")
{
CrossLinkSPtr cross_link_sp =
std::make_shared<CrossLink>(cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This is the CFP-chromophore cross-link");
AND_WHEN(
"The cross-link is actually created by adding Monomer instances")
{
bool ok = false;
// Failing addition:
cross_link_sp->fillInMonomers("", ok);
REQUIRE_FALSE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 0);
// And now the real one
cross_link_sp->fillInMonomers(";66;67;", ok);
THEN("The Monomer instances are correctly set")
{
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
REQUIRE(cross_link_sp
->continuumOfLocationsOfInclusiveSequenceMonomersAsText(
Enums::LocationType::INDEX)
.toStdString() == ";66;67;");
}
AND_WHEN("Another Monomer instance is set also")
{
MonomerSPtr third_monomer_sp =
polymer_sp->getSequenceCstRef().getMonomerCstSPtrAt(68);
cross_link_sp->appendMonomer(third_monomer_sp);
THEN("The new Monomer instance is set correctly and all are there")
{
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 3);
REQUIRE(cross_link_sp->getMonomersRef().size() == 3);
REQUIRE(cross_link_sp
->continuumOfLocationsOfInclusiveSequenceMonomersAsText(
Enums::LocationType::INDEX)
.toStdString() == ";66;67;68;");
std::vector<std::size_t> extreme_locations =
cross_link_sp->locationssOfOnlyExtremeSequenceMonomers(
Enums::LocationType::INDEX);
REQUIRE(extreme_locations.front() == 66);
REQUIRE(extreme_locations.back() == 68);
REQUIRE(cross_link_sp
->locationsOfOnlyExtremeSequenceMonomersAsText(
Enums::LocationType::INDEX)
.toStdString() == ";66;68;");
MonomerCstSPtr first_monomer_csp = cross_link_sp->getMonomerAt(0);
REQUIRE(cross_link_sp->getFirstMonomer() == first_monomer_csp);
REQUIRE(cross_link_sp->monomerIndex(first_monomer_csp, ok) == 0);
REQUIRE(
cross_link_sp->monomerIndex(first_monomer_csp.get(), ok) == 0);
REQUIRE(ok);
MonomerCstSPtr second_monomer_csp =
cross_link_sp->getMonomerAt(1);
REQUIRE(cross_link_sp->monomerIndex(second_monomer_csp, ok) == 1);
REQUIRE(
cross_link_sp->monomerIndex(second_monomer_csp.get(), ok) == 1);
REQUIRE(ok);
REQUIRE(polymer_sp->getSequenceCstRef().monomerIndex(
first_monomer_csp, ok) == 66);
REQUIRE(ok);
REQUIRE(polymer_sp->getSequenceCstRef().monomerIndex(
second_monomer_csp, ok) == 67);
REQUIRE(ok);
AND_THEN("Removing and readding the last Monomer should work")
{
cross_link_sp->removeMonomerAt(2);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
cross_link_sp->appendMonomer(third_monomer_sp);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 3);
}
THEN("The mass of the CrossLink can be computed")
{
REQUIRE_THAT(
cross_link_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(-20.0262147493, 0.0000000001));
REQUIRE_THAT(
cross_link_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(-20.0311745907, 0.0000000001));
double mono = 1000;
double avg = 1001;
cross_linker_csp->accountMasses(mono, avg, 3);
REQUIRE_THAT(mono,
Catch::Matchers::WithinAbs(
1000 - (20.0262147493 * 3), 0.0000000001));
REQUIRE_THAT(avg,
Catch::Matchers::WithinAbs(
1001 - (20.0311745907 * 3), 0.0000000001));
AND_WHEN(
"The CrossLink is actually performed onto the Polymer's "
"Monomer "
"instances")
{
polymer_sp->crossLink(cross_link_sp);
THEN("The CrossLink must be found in the Polymer")
{
REQUIRE(polymer_sp->getCrossLinksCstRef().size() == 1);
}
AND_WHEN(
"Configuring calculation options NOT to account for "
"cross-links")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::NONE,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(0, 240 - 1));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->getCrossLinksCstRef().size() == 1);
REQUIRE(polymer_sp->calculateMasses(calc_options,
/*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(
26885.5345715247, 0.0000000001));
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(
26902.1945837392, 0.0000000001));
}
AND_WHEN(
"Configuring calculation options to account for "
"cross-links")
{
REQUIRE(polymer_sp->getCrossLinksCstRef().size() == 1);
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::CROSS_LINKER,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(0, 240 - 1));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->getCrossLinksCstRef().size() ==
1);
REQUIRE(polymer_sp->calculateMasses(calc_options,
/*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(
26865.5083567754, 0.0000000001));
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(
26882.1634091485, 0.0000000001));
}
}
}
}
}
}
}
}
}
}
}
}
}
}
SCENARIO(
"Construction of a set of 7 CrossLink instances and use with a pristine "
"Polymer",
"[CrossLink]")
{
test_utils_1_letter_cross_link.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_cross_link.msp_polChemDef;
QString polymer_file_path =
QString("%1/polymer-sequences/%2")
.arg(TESTS_INPUT_DIR)
.arg("kunitz-inhibitor-human-no-cross-link.mxp");
GIVEN("A Polymer instance created by loading an XML file")
{
PolymerSPtr polymer_sp = Polymer::createSPtr(pol_chem_def_csp);
REQUIRE(polymer_sp->renderXmlPolymerFile(polymer_file_path));
REQUIRE(polymer_sp->size() == 352);
AND_GIVEN("An allocated CrossLinker as found in the PolChemDef by name")
{
CrossLinkerCstSPtr cross_linker_csp =
pol_chem_def_csp->getCrossLinkerCstSPtrByName("DisulfideBond");
REQUIRE(cross_linker_csp != nullptr);
REQUIRE(cross_linker_csp->getPolChemDefCstSPtr() == pol_chem_def_csp);
// Now allocated seven "DisulfideBond" CrossLinks
// THESE ARE POSITIONS, NOT INDICES
// DisulfideBond/;91;188
// DisulfideBond/;231;281
// DisulfideBond/;240;264
// DisulfideBond/;256;277
// DisulfideBond/;287;337
// DisulfideBond/;296;320
// DisulfideBond/;312;333
bool ok = false;
CrossLinkSPtr cross_link_sp = std::make_shared<CrossLink>(
cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This one of the DisulfideBond cross-links");
cross_link_sp->fillInMonomers(";90;187;", ok);
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
polymer_sp->crossLink(cross_link_sp);
cross_link_sp = std::make_shared<CrossLink>(
cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This one of the DisulfideBond cross-links");
cross_link_sp->fillInMonomers(";230;280;", ok);
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
polymer_sp->crossLink(cross_link_sp);
cross_link_sp = std::make_shared<CrossLink>(
cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This one of the DisulfideBond cross-links");
cross_link_sp->fillInMonomers(";239;263;", ok);
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
polymer_sp->crossLink(cross_link_sp);
cross_link_sp = std::make_shared<CrossLink>(
cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This one of the DisulfideBond cross-links");
cross_link_sp->fillInMonomers(";255;276;", ok);
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
polymer_sp->crossLink(cross_link_sp);
cross_link_sp = std::make_shared<CrossLink>(
cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This one of the DisulfideBond cross-links");
cross_link_sp->fillInMonomers(";286;336;", ok);
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
polymer_sp->crossLink(cross_link_sp);
cross_link_sp = std::make_shared<CrossLink>(
cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This one of the DisulfideBond cross-links");
cross_link_sp->fillInMonomers(";295;319;", ok);
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
polymer_sp->crossLink(cross_link_sp);
cross_link_sp = std::make_shared<CrossLink>(
cross_linker_csp,
polymer_sp->getCstSharedPtr(),
"This one of the DisulfideBond cross-links");
cross_link_sp->fillInMonomers(";311;332;", ok);
REQUIRE(ok);
REQUIRE(cross_link_sp->getMonomersCstRef().size() == 2);
MonomerCstSPtr monomer_csp =
polymer_sp->getSequenceCstRef().getMonomerCstSPtrAt(311);
REQUIRE(ok);
REQUIRE(monomer_csp != nullptr);
REQUIRE(cross_link_sp->hasUuid(monomer_csp));
QString uuid = cross_link_sp->getUuidForMonomer(monomer_csp);
MonomerCstSPtr same_monomer_csp = cross_link_sp->getMonomerForUuid(uuid);
REQUIRE(same_monomer_csp == monomer_csp);
std::vector<QString> all_monomer_uuids = cross_link_sp->getAllMonomerUuids();
REQUIRE(all_monomer_uuids.size() == 2);
polymer_sp->crossLink(cross_link_sp);
WHEN("The polymer has been cross-linked with the CrossLink instances")
{
THEN("The CrossLink instances must be found in the Polymer")
{
REQUIRE(polymer_sp->getCrossLinksCstRef().size() == 7);
std::size_t in_count;
std::size_t out_count;
AND_THEN("Encompassing logic can be tested")
{
// THESE ARE POSITIONS, NOT INDICES
// DisulfideBond/;91;188
// DisulfideBond/;231;281
// DisulfideBond/;240;264
// DisulfideBond/;256;277
// DisulfideBond/;287;337
// DisulfideBond/;296;320
// DisulfideBond/;312;333
std::vector<std::size_t> monomer_indices =
polymer_sp->getCrossLinksCstRef()
.at(0)
->continuumOfLocationsOfInclusiveSequenceMonomers(
Enums::LocationType::INDEX);
REQUIRE(monomer_indices.size() == 188 - 91 + 1);
REQUIRE(monomer_indices.at(0) == 90);
REQUIRE(monomer_indices.at(97) == 187);
REQUIRE(polymer_sp->getCrossLinksCstRef().at(0) != nullptr);
REQUIRE(
polymer_sp->getCrossLinksCstRef()
.at(0)
->isEncompassedByIndexRange(90, 187, in_count, out_count) ==
Enums::CrossLinkEncompassed::FULLY);
REQUIRE(
polymer_sp->getCrossLinksCstRef()
.at(0)
->isEncompassedByIndexRange(91, 187, in_count, out_count) ==
Enums::CrossLinkEncompassed::PARTIALLY);
REQUIRE(
polymer_sp->getCrossLinksCstRef()
.at(0)
->isEncompassedByIndexRange(90, 186, in_count, out_count) ==
Enums::CrossLinkEncompassed::PARTIALLY);
REQUIRE(
polymer_sp->getCrossLinksCstRef()
.at(0)
->isEncompassedByIndexRange(92, 187, in_count, out_count) ==
Enums::CrossLinkEncompassed::PARTIALLY);
REQUIRE(
polymer_sp->getCrossLinksCstRef()
.at(0)
->isEncompassedByIndexRange(92, 186, in_count, out_count) ==
Enums::CrossLinkEncompassed::NOT);
}
THEN(
"The copy-constructor and assignment-based CrossLink creation can "
"be tested thoroughly")
{
CrossLink another_cross_link(*cross_link_sp);
CrossLink other_cross_link;
other_cross_link = another_cross_link;
REQUIRE(other_cross_link == *cross_link_sp);
REQUIRE_FALSE(other_cross_link != *cross_link_sp);
REQUIRE(other_cross_link.isValid());
double mono = 0;
double avg = 0;
REQUIRE(other_cross_link.calculateMasses(
pol_chem_def_csp->getIsotopicDataCstSPtr(), mono, avg));
REQUIRE_THAT(
mono, Catch::Matchers::WithinAbs(-2.01565006453, 0.0000000001));
QString expected_text =
"\nCross-link:\n===============\nCross-linker name: "
"DisulfideBond\nCross-link comment: This one of the "
"DisulfideBond cross-links\nPartner 1: C at position: "
"312\nPartner 2: C at position: 333\n";
REQUIRE(cross_link_sp->prepareResultsTxtString().toStdString() ==
expected_text.toStdString());
}
}
AND_WHEN(
"Configuring calculation options NOT to account for cross-links")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::NONE,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(0, polymer_sp->size() - 1));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options, /*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(38973.9813242497, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(38999.3128988044, 0.0000000001));
}
AND_WHEN(
"Configuring calculation options to account for cross-links")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::CROSS_LINKER,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(0, polymer_sp->size() - 1));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options,
/*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(38959.8717737979, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(38985.2017182470, 0.0000000001));
}
}
WHEN(
"Configuring calculation options to account for "
"cross-links "
"with only one fully encompassed")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::CROSS_LINKER,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(55, 216));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options,
/*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(18241.1791940081,
0.0000000001));
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(18252.6111982139,
0.0000000001));
}
}
}
WHEN(
"Configuring calculation options to account for "
"cross-links "
"with more than one fully encompassed")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::CROSS_LINKER,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(72, 284));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options,
/*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(23696.2700807047,
0.0000000001));
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(23711.5168000099,
0.0000000001));
}
}
WHEN(
"Configuring calculation options to account for "
"cross-links "
"with more than one fully encompassed")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::CROSS_LINKER,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(196, 283));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options,
/*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(9571.3824122666,
0.0000000001));
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(9577.7946954897,
0.0000000001));
}
}
}
WHEN(
"Configuring calculation options to account for "
"cross-links "
"with two incomplete cross-links")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::CROSS_LINKER,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(155, 286));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options,
/*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(14356.6660883098,
0.0000000001));
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(14366.1307048399,
0.0000000001));
}
}
}
}
}
}
}
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
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